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EIF to Fund Breast Cancer Biomarker-Discovery Project

Seven biomedical research institutions will use a three-year, $9 million award from the Entertainment Industry Foundation's Women's Cancer Research Fund to discover biomarkers associated with early stage breast cancer, the EIF said this week.

According to the EIF, the philanthropic arm of the entertainment industry, the seven partners have joined together to form the EIF/WCRF Breast Cancer Biomarker Discovery Project.

The project will be led by researchers at the Fred Hutchinson Cancer Research Center, and will also include the Pacific Northwest Research Laboratory, Dana Farber Cancer Institute, the University of Southern California's Norris Comprehensive Cancer Center and Hospital, the Institute for Systems Biology, the Broad Institute, and the University of Texas' MD Anderson Cancer Center, the EIF said.


NCI to Issue Two Proteomics-Based RFPs This Fall

The National Cancer Institute plans to issue a pair of RFPs this fall as part of its Clinical Proteomic Technologies Initiative (see ProteoMonitor 7/8/2005).

The CPTI is an "integrated approach to develop and enhance proteomic technology capabilities to support the reliable discovery and measurement of cancer-associated proteins from readily accessible biological fluids," NCI said on its web site.

The first RFP will aim to create multiple 5-year awards to establish the Clinical Proteomic Technology Assessment Consortia through NIH U24 cooperative agreement funding mechanisms. The goal of the consortia will be "to optimize and standardize proteomic technology platforms, with an emphasis on mass spectrometry (MS)-based and affinity capture-based approaches," NCI said on its web site.

As part of the research, multidisciplinary teams will be required to address technology engineering, statistical design, and quantitative pathological assessments as applied to furthering our understanding of basic and clinical mechanisms of cancer, NCI said. A "key component" of the consortia will be to develop inter-laboratory protocols and analysis of biological samples from both mouse models and clinical specimens.

The CPTAC programs will support two overarching aims: to "develop and refine MS-based and affinity capture-based proteomic platforms to improve key factors such as experimental reproducibility, specificity, and mass accuracy, dynamic range, peptide/protein identification, individual peptide/protein quantification, sample throughput, and per sample/unit cost;" and "to develop a systematic assessment of the procedures and methodologies to minimize variability in MS and affinity capture-based measurements and data analyses," NCI said.

"Through standardizations and improvements, the CPTACs should aim to collectively identify and validate at least 1000 reproducible features of interest in cancer biospecimens by the end of the 5-year program and, at the same time, identify technologically superior platforms for MS-based and affinity capture-based proteomic analyses," NCI said.

These consortia will also "serve as critical sources of protocol development, education, and training to support standardized proteomic research platforms across the cancer research enterprise," NCI added.

Click here for more information about this RFP.

The second RFP will aim to "support investigator-initiated projects in Advanced Proteomic Platforms, Analytical Methods, and Computational Sciences to overcome current barriers in protein/peptide feature detection, identification, and quantification and develop mathematical, computational, and predictive approaches for the analysis and facile exchange of large-scale proteomic data," according to NCI.

The program is intended to "improve the development of technological and computational platforms that advance the performance of proteomic detection and identification in complex biological mixtures from mouse models and clinical specimens," NCI said.

Applicants "should demonstrate strong capabilities in statistical analysis and quality assurance of data. The R01 grant mechanism will be used to support bioinformatics and computational science programs, whereas the R21 and R33 mechanisms will be used to support the proteomic technology platforms. The goals of these projects include (but are not limited to) increased instrumental resolution capabilities, development of novel or advanced peptide/protein discovery technologies, integration of data and results from different analysis platforms, validation of proteomic methods and technologies, and improvements in data-mining algorithms and data-exchange formats."

The CPTI will "support the development of standards, resources, and clinical proteomic platforms for cancer research by harnessing efforts to establish standard references, quality control measures, and informatics platforms capable of aggregating and comparing data," NCI said.

Click here for this RFP.

These funding opportunities will be open to US-based academic, nonprofit, and for-profit institutions. NCI added that foreign institutions may be invited by eligible applicants to participate as subcontractors.


DOE Awards $92M to Six Genomic, Proteomic Projects to Study Microbes

The Department of Energy has awarded a total of $92 million to six collaborative research projects under its Office of Science's Genomics GTL research program, DOE said this week.

The six projects, involving 75 senior scientists at 21 institutions, aim to better understand microbes and microbial communities.

The following projects will receive funding:

  • Genome-Based Models to Optimize In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Waste Organic Matter, led by the University of Massachusetts, Amherst, will receive $21.8 million over five years;
  • Proteogenomic Approaches for the Molecular Characterization of Natural Microbial Communities, led by the University of California, Berkeley, will receive $10.5 million over five years;
  • Dynamic Spatial Organization of Multi-Protein Complexes Controlling Microbial Polar Organization, Chromosome Replication, and Cytokinesis, led by Stanford University, will receive $17.9 million over five years;
  • High Throughput Identification and Structural Characterization of Multi-Protein Complexes During Stress Response in Desulfovibrio vulgaris, led by Lawrence Berkeley National Laboratory, will receive $25.8 million over five years;
  • Molecular Assemblies, Genes, and Genomics Integrated Efficiently, led by Lawrence Berkeley National Laboratory, will receive $12.9 million over five years; and
  • An Integrated Knowledge Resource for the Shewanelle Federation, led by Oak Ridge National Laboratory, will receive $3 million over three years.

GSK Licenses Prolexys' Protein Interaction Database

GlaxoSmithKline has inked a non-exclusive license to access Prolexys' protein-protein interaction database, the company said this week.

The database, which Prolexys calls the Human Interactome, contains more than 258,000 human protein-protein interactions, Prolexys said.

Financial terms of the deal were not disclosed.


ABI/MDS Sciex Sell 21 Mass Specs to CDC, State Health Labs

Applied Biosystems and its joint venture partner MDS Sciex have sold 21 mass spectrometry systems to the Centers for Disease Control and Prevention and several state health laboratories as part of their Laboratory Response Network, a nationwide network of labs to detect biological and chemical threats, ABI said this week.

The labs will use the API 4000 LC/MS/MS systems to identify toxic chemicals in human blood or urine samples.

ABI has already supplied real-time PCR systems to the Laboratory Response Network for biological detection, according to the company.


Michigan State University Lands $4M Grant to Study Function of 4,400 Arabidopsis Genes

A collaboration of researchers from Michigan State University has received a $4 million grant from the National Science Foundation to study the functions of 4,400 Arabidopsis genes , MSU said on last week.

Under the four-year project, the scientists will focus on nuclear genes that encode chloroplast proteins. The grant is part of NSF's Arabidopsis 2010 project (see story), a worldwide effort to catalogue the function of every gene in the plant.

The project will create eight full-time jobs for technicians, graduate students, postdocs, and fellows.


Celliance Acquires Gene-Expression Technology from Innovata

Celliance has acquired a gene-expression technology from Innovata for an undisclosed amount, the Serologicals subsidiary said this week.

The so-called ubiquitous chromatin opening element technology allows researchers to improve the yield, consistency, and stability of protein production in cultured mammalian cells. Other applications include gene therapy, transgenics, and the generation of cell lines for drug screening, according to Celliance.

The technology has been licensed by a number of pharmaceutical and biotechnology companies, including Medarex and Maxygen.


Invitrogen to Make Sequence Analysis Software Free for Nonprofit Labs

Invitrogen has created a Vector NTI Open Access policy and the online Vector NTI User Community in conjunction with the release of Vector NTI Advance 10, the latest version of its NTI sequence analysis software, the firm said last week.

According to the company, the Open Access policy will enable researchers in not-for-profit laboratories to apply for free, annual, and renewable licenses of Vector NTI. The User Community is designed to serve as an online meeting place for researchers to acquire the latest versions of the software, obtain technical resources, and communicate with Invitrogen and other users, Invitrogen said.

Greg Lucier, chairman and CEO of Invitrogen, said the company anticipates "having tens of thousands of users in the academic, government and research institutions take advantage of our Open Access policy."

Invitrogen said that the Wellcome Trust Sanger Institute and The Scripps Research Institute are both Open Access participants.

ProteoMonitor's sister publication BioInform reported on the developments surrounding Vector NTI two weeks ago.


PerkinElmer to Sell GeneEd Online Life Sciences Course

PerkinElmer will use GeneEd's custom eLearning capabilities and will resell catalog eLearning courses globally, the company said this week.

GeneEd has already developed an "atomic absorption" course for PerkinElmer, and plans to develop a course for "inductively coupled plasma and chromatography systems," GeneEd said.

In addition, PerkinElmer customers will have access to GeneEd's catalog of biopharma technology courses through PerkinElmer's website.

Financial terms of the agreement were not disclosed.

The Scan

Response Too Slow, Cautious

A new report criticizes the global response to the threat of the COVID-19 pandemic, Nature News reports.

Pushed a Bit Later

Novavax has pushed back its timeline for filing for authorization for its SARS-CoV-2 vaccine, according to Bloomberg.

AMA Announces Anti-Racism Effort

The Associated Press reports that the American Medical Association has released a plan to address systemic racism in healthcare.

Nucleic Acids Research Papers on miRMaster 2.0, MutationTaster2021, LipidSuite

In Nucleic Acids Research this week: tool to examine small non-coding RNAs, approach to predict ramifications of DNA variants, and more.